The Many are a race of hive minded parasites that superficially resemble giant liver flukes. Once a human is infected by the parasitic worm released by a large, leathery egg, the genetically female Annelid takes up residence in their chest cavity, feeding on them internally, and releasing stress hormones that increase the production of adrenaline and endorphins, causing the host to become irritable, and fusing her DNA with her hosts (genetic recombination). This causes tumors to form. Once the Annelid has eaten enough, she bursts out of the chest and attaches to the forehead, killing the host. However, the Annelid takes over cognitive and motor functions, turning the human into a zombie-like Hybrid. The most the remaining human personality can do is babble non-sense phrases, demands for non-infected to join the hive mind, or, tragically, beg to be killed or warn non-infected to run away. The Hybrid eventually metamorphoses into a hulking beast known as a Rumbler, which has the human remains hanging off one of its shoulders. The Rumbler's purpose is to gain bio-matter, in order to feed it's brain, which is developing into a Psi Reaver. Once the Psi Reaver hatches, the Rumbler is recycled. Some eggs produce the genetically male, wasp-like Swarm. If these mate with the Annelid attached to a human host, the Hybrids development into a Rumbler is arrested, and the Hybrid is instead converted into a number of genderless Arrachnids. The Many is a name the hive mind chose for itself; the game refers to them as "Annelids."

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Once SHODAN ejected the module, it travelled to Tau Ceti V over a period of 30 years. The mutants trapped inside continued to evolve, developing into parasitic worms. In 2114, the Von Braun, paired with the security vessel UNN Rickenbacker, using it's hyperdrive, travelled to Tau Ceti V in a period of three weeks, and took up orbit above Tau Ceti V. They received a radio signal from the planets surface. Believing the signal to be from an alien civilization attempting peaceful communication, the Von Braun sent a contact team to the surface. Instead of a diplomatic team from any civilization, they found a clutch of fleshy pods-Annelid Eggs- and a computer storage module. Taking these to the Von Braun for study, several crew members and Marines were infected by Annelids. One human, under the influence of the Many's telepathy, hacked into the Von Brauns master computer, XERXES. A copy of SHODAN, contained in the storage module, escaped into the computers contained in Dr. Polido's office, and instructed the medical team of the Von Braun to perform illegal cybernetic augmentations on a marine designated SOLDIER-G65434-2, nicknamed "Goggles" due to the large cameras replacing his eyes. SOLDIER-G65434-2 began to disrupt the Many's activities on the Von Braun, including killing the clutch of eggs deposited in its Hydroponics deck, the tendrils of biomass clogging the Von Brauns elevator system and re-programmiong the subverted simulation units controlling XERXES. Eventually, he travelled, in an escape pod, into the Body of the Many, where he killed the Brain of the Many, stopping their threat to earth.